RetrogeneDB ID: retro_mdom_904

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 2:371158351..371158726(-)
• Located in intron of: ENSMODG00000023357

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: FAM195B
• Ensembl ID: ENSMODG00000002923
• Aliases: None
• Description: family with sequence similarity 195, member B [Source:HGNC Symbol;Acc:28007]

Sequence

>retro_mdom_904
TCTGAAACTGGGCAAGCAGTTGTCCTTCTCAACAGCAGCTGGAAGCCAAGGAGGAGACCCAAGCATTCAAGTTGTGTGAT
TGGATCAGACACCCCCAGCTATGACCAATTCCCCGTCTCCAGAGTCGTCTACAATGGCAGAAGGAATAGTTGCCCCCAGT
CTCCAAGCAACAGCAGTGAGATCTTCACTCCGGCCCATGAGGAGAGCGTGCGCTTCATTGAAGCATGGCAGTGTGTGGAA
CGAGACCTCCGGAACCAGATGTCTGGCAGCAAGCGTGTTCTGGTGGACAAAGTCCCTAACCTCAGTCTGAAGACTTTCAA
ACCTTTTGACTTGAGTGGCCTGAAATGCCAGAACACACAAGATGCCAAGAAGTCC

Alignment

ORF - retro_mdom_904 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.54 %
• Parental protein coverage: 57.27 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SETGRAVALLNSSLKPRRRPKHSSCVIGSDTPAMTSSPVSRVVYNGKRNSSPRSPSNSSEIFTPAHEENV
          SETG.AV.LLNSS.KPRRRPKHSSCVIGSDTP.....PVSRVVYNG.RNS.P.SPSNSSEIFTPAHEE.V
Retrocopy SETGQAVVLLNSSWKPRRRPKHSSCVIGSDTPSYDQFPVSRVVYNGRRNSCPQSPSNSSEIFTPAHEESV

Parental  RFIYEAWQCVERDLRNQMSGSERGLVEEYVEKVPNPSLKTFKPFDLSDLKRRNTQDAKKS
          RFI.EAWQCVERDLRNQMSGS.R.LV.....KVPN.SLKTFKPFDLS.LK..NTQDAKKS
Retrocopy RFI-EAWQCVERDLRNQMSGSKRVLVD----KVPNLSLKTFKPFDLSGLKCQNTQDAKKS

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP007412_brain	0.00 RPM	0.00 RPM
SRP007412_cerebellum	0.00 RPM	0.00 RPM
SRP007412_heart	0.00 RPM	0.00 RPM
SRP007412_kidney	0.00 RPM	0.00 RPM
SRP007412_liver	0.00 RPM	0.00 RPM
SRP007412_testis	0.00 RPM	0.00 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_904 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_904 was not experimentally validated.

Homology

Retrocopy orthology:

Monodelphis domestica does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000002923	1 retrocopy	retro_mdom_904 ,
Rattus norvegicus	ENSRNOG00000036691	1 retrocopy	retro_rnor_1285,